13-99429512-C-T

Variant names:

• chr13-99429512-C-T
• rs9585056
• ENST00000646895.1:n.887G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000646895.1(ENSG00000285448):​n.887G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.71 in 152,008 control chromosomes in the GnomAD database, including 38,765 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.71 (38765 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000285448 ENST00000646895.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.17

Genes affected

ENSG00000285448 (HGNC:56890):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.912 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285448	ENST00000646895.1	n.887G>A		non_coding_transcript_exon_variant	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.710 AC: 107855 AN: 151890 Hom.: 38747 Cov.: 32

Gnomad AFR AF: 0.597

Gnomad AMI AF: 0.806

Gnomad AMR AF: 0.708

Gnomad ASJ AF: 0.737

Gnomad EAS AF: 0.934

Gnomad SAS AF: 0.683

Gnomad FIN AF: 0.759

Gnomad MID AF: 0.715

Gnomad NFE AF: 0.753

Gnomad OTH AF: 0.724

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 2 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

Gnomad4 FIN exome AF: 0.00

GnomAD4 genome AF: 0.710 AC: 107918 AN: 152008 Hom.: 38765 Cov.: 32 AF XY: 0.711 AC XY: 52838 AN XY: 74304

Gnomad4 AFR AF: 0.597

Gnomad4 AMR AF: 0.707

Gnomad4 ASJ AF: 0.737

Gnomad4 EAS AF: 0.934

Gnomad4 SAS AF: 0.685

Gnomad4 FIN AF: 0.759

Gnomad4 NFE AF: 0.753

Gnomad4 OTH AF: 0.724

Alfa AF: 0.743 Hom.: 38475

Bravo AF: 0.706

Asia WGS AF: 0.770 AC: 2681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.31
DANN	Benign	0.73

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9585056; hg19: chr13-100081766;